|
| Status |
Public on Jun 30, 2015 |
| Title |
Mesenchymal stromal cell, osteosarcoma patient, sample 002 |
| Sample type |
RNA |
| |
|
| Source name |
Osteosarcoma patient MSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal stromal cells
gender: female
age: 13
|
| Growth protocol |
Bone marrow derived mononuclear cells were obtained from 5 to 15 ml of heparinized bone marrow aspirate by density gradient centrifugation on Ficoll. Cells were plated on non-coated 75 cm2 polystyrene flasks at a cell density of 160000/cm2 in complete culture medium (LG-DMEM [Invitrogen, Paisley, United Kingdom] supplemented with penicillin and streptomycin [merk] and 10% fetal bovine serum [FBS; HyClone, Verviers, Belgium]). We used a characterized and defined FBS batch preselected for its potential to support MSC expansion and continued to use this specific batch throughout the culture period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from frozen cell pellets of at least 1*10e6 undifferentiated mesenchymal stem cells at passage 2 to 5 using TRIzol reagent (Invitrogen). Cells were lysed in TRIzol, followed by phase separation in chloroform (merk), precipitation using 2-propanolol (merk) and washing in 75% ethanol. RNA clean-up was performed using the Qiagen Rneasy mini kit with on-column DNAse treatment. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer and Nanodrop ND-1000, respectively.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
As per manufacturer's instructions.
|
| Scan protocol |
As per manufacturer's instructions.
|
| Description |
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).
|
| Data processing |
Microarray data were normalized using the Cubic Spline normalization method with the Illumina BeadStudio Gene Expression Module (Illumina). Statistical analysis of microarray was performed using Significance Analysis for Microarrays (SAM)
|
| |
|
| Submission date |
Nov 28, 2012 |
| Last update date |
Jul 01, 2015 |
| Contact name |
Marieke Lydia Kuijjer |
| Organization name |
Centre for Molecular Medicine Norway
|
| Lab |
Kuijjer
|
| Street address |
Gaustadalléen 21
|
| City |
Oslo |
| ZIP/Postal code |
0349 |
| Country |
Norway |
| |
|
| Platform ID |
GPL13376 |
| Series (1) |
| GSE42572 |
Gene expression analysis of mesenchymal stromal cells obtained from healthy donors and osteosarcoma patients |
|
